ASGAL (Alternative Splicing Graph ALigner) is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation. The main idea behind ASGAL is the following one: the alternative splicing events can be detected by aligning the RNA-Seq reads against the splicing graph of the gene.

The instructions to install and use ASGAL are at http://asgal.algolab.eu

• git
• python3
• gffutils
• biopython
• cmake

git clone https://github.com/AlgoLab/galig.git
cd galig
make prerequisites
make

./asgal -g [genome] -a [annotation] -s [sample] -o output

In more detail:

# Align RNA-Seq reads to a splicing graph
./bin/SpliceAwareAligner -g [reference] -a [annotation] -s [sample] -o output.mem

# Convert alignments to SAM format
python3 ./scripts/formatSAM.py -m output.mem -g [reference] -a [anotation] -o output.sam

# Detect events from alignments
python3 ./scripts/detectEvents.py -g [reference] -a [annotation] -m output.mem -o output.events.csv

cd example
tar xfz input.tar.gz
../asgal -g ./input/genome.fa -a ./input/annotation.gtf -s ./input/reads.fasta -o output

This command will produce three files:

• output.mem, containing the alignments to the splicing graph
• output.sam, containing the alignments to the splicing graph mapped to the reference genome
• output.events, containing the alternative splicing events detected in the RNA-Seq sample

An extended explanation of this example can be found here.

The tool has been tested only on 64bit Linux system. You can find more information at http://asgal.algolab.eu.